Collman15v2 Gaba comparisons using Maximum in cube of size <=0.5 micron

1 MEDA run

Loading the class labels sent by Forrest

cl <- read.csv("cleft_class.csv")[-18,]
fmax <- read.csv("collman15v2_Fmax_20171214.csv")
sfmax <- scale(fmax, center = TRUE, scale = TRUE)

loc <- read.csv("locations_collman15v2_Fmax_20171214.csv")

table(cl$gaba)

## 
##   0   1 
## 214  22

table(cl$postgaba)

## 
##   0   1 
## 212  24

#ccol <- read.csv("params.csv")[1,-c(1,14)]
ccol <- c('blue', 'blue', 'blue', 'red', 'red', 'red', 'black', 'black', 'green', 'green', 'green', 'green')
set.seed(1234)

L <- list()
L[[1]] <- mlocation(fmax, ccol = ccol)
L[[2]] <- d1heat(sfmax, ccol = ccol)
L[[3]] <- cumvar(sfmax)
L[[4]] <- outliers(sfmax)
L[[5]] <- pairhex(sfmax, ccol = ccol)
L[[6]] <- medacor(fmax, ccol = ccol)
set.seed(1234)
L[[7]] <- hmc(sfmax, ccol = ccol,
              maxDepth = 2)
plot(L[[7]])

1.1 mlocation

1.2 d1heat

1.3 cumvar

1.4 outliers

1.5 pairhex

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : pseudoinverse used at 0.28334

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : neighborhood radius 0.44283

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## FALSE, : reciprocal condition number 0

1.6 correlation

1.7 dendrogram

##      1      2 
## 0.7076 0.2924

1.8 pairs plots

1.9 stacked means

1.10 cluster means

2 Set \(K = 2\)

Here we restrict our hierarchical GMM function to one split only and then compare with the true gaba/non-gaba class labels.

set.seed(1030)
h2 <- hmc(sfmax, maxDepth = 2, modelNames = 'VVE')
l2 <- h2$dat$labels$col - 1
p0 <- mclust::adjustedRandIndex(l2, cl$gaba)

perms <- foreach(i = 1:1e4, .combine = c) %dopar% {
  set.seed(i*2)
  mclust::adjustedRandIndex(sample(l2), cl$gaba)
}

tmp <- h2$dat$labels$col
pairs(h2$dat$data, 
      col = viridis(max(tmp))[tmp],
      pch = 19, cex = 0.5, main = "colored by prediction")

pairs(h2$dat$data, 
      col = c('darkblue', 'violet')[cl$gaba +1],
      pch = 19, cex = 0.5, main = "colored by truth")

plotDend(h2)

##      1      2 
## 0.8475 0.1525

stackM(h2, depth = 2, centered = TRUE, ccol = ccol)

hist(perms, xlim = c(min(perms), p0 + 0.25*p0),
     main = "permutation test of ARI values")
abline(v = p0, col = 'red')

df1 <- data.frame(loc)
df1$gaba <- as.factor(cl$gaba)
df1$classification <- as.factor(tmp -1)
df1$correct_classification <- (df1$classification == df1$gaba)
df1$TN <- (df1$classification == 0 & df1$gaba == 0)
df1$FN <- (df1$classification == 0 & df1$gaba == 1)
df1$FP <- (df1$classification == 1 & df1$gaba == 0)
df1$TP <- (df1$classification == 1 & df1$gaba == 1)
#df1$text <- links

p1 <- ggplot(df1, aes(x = x, y=y,z=z, col = gaba, shape =
                      correct_classification)) + 
  facet_wrap(~ z, ncol = 6) +
  geom_point()

p1

2.0.1 same as above with interactivity

ggplotly(p1)

#p2 <- plot_ly(df1, x = ~x, y = ~y, color = ~gaba,
#             hoverinfo = 'text',
#               text = ~links)
#p2
#
#htmlwidgets::saveWidget(as_widget(p2), "links.html")

2.0.2 Confusion matrix (classfication on rows)

(ta <- table(classification = tmp-1, df1$gaba))

##               
## classification   0   1
##              0 180  20
##              1  34   2

The above table shows that out of 22 true gaba synapses 20 were mis-classified as non-gaba synapses.

3 NDVIZ Links

Note that the centroids are caluclated from the annotations which means that the centorid might not be in an area with annotated pixels.

3.1 False Negatives (synaptograms here)

FalseNegatives
2163, 892, 2
6002, 2969, 25
3993, 2950, 20
6174, 1854, 25
3800, 2549, 20
4060, 2599, 13
3553, 4245, 21
1070, 3472, 24
1666, 3290, 18
1103, 2926, 12
914, 3286, 19
993, 2979, 14
479, 3478, 20
3385, 3538, 14
89, 2717, 13
5003, 1431, 13
4523, 2483, 5
734, 2080, 12
3292, 4462, 22
3490, 4476, 21

3.2 False Positives (some synaptograms here)

FalsePositives
3565, 3207, 1
2999, 3356, 1
2691, 3820, 0
2079, 4014, 0
3525, 2414, 1
3231, 1826, 4
4440, 3234, 0
5102, 2540, 0
4029, 2877, 1
1518, 1855, 1
4332, 1215, 1
5097, 1103, 1
3196, 534, 1
813, 3796, 1
1030, 2559, 0
1606, 3000, 2
3633, 577, 1
4357, 896, 1
5545, 3306, 3
3514, 3550, 1
1130, 1386, 0
3184, 2673, 0
883, 2296, 2
5597, 2381, 2
1590, 2291, 3
4435, 3060, 3
5141, 707, 4
5837, 2975, 2
4212, 3355, 4
4164, 3620, 4
4748, 905, 4
1922, 4140, 2
2461, 4070, 4
5470, 2417, 4

3.3 True Negatives

TrueNegatives
2137, 3803, 1
2417, 3384, 2
2036, 2401, 4
458, 2538, 2
1344, 3292, 2
4543, 1195, 2
4339, 506, 3
4970, 3472, 4
4597, 3678, 4
764, 2557, 5
1427, 1487, 6
4068, 1731, 4
118, 1145, 6
5447, 4249, 25
5816, 4134, 24
4874, 4130, 25
4306, 3978, 26
5188, 4078, 23
5267, 3637, 22
4771, 3289, 20
5646, 2647, 24
5877, 2918, 22
4968, 2977, 16
6071, 1825, 26
6111, 1644, 26
5567, 1785, 24
4393, 2188, 18
4582, 2195, 26
5620, 1488, 25
4853, 1339, 25
4411, 1315, 26
5895, 1168, 23
5411, 1105, 22
5336, 632, 19
5693, 850, 17
5457, 629, 13
4379, 909, 26
4184, 815, 26
3217, 1429, 26
2959, 1793, 23
3534, 1542, 20
3703, 893, 15
3849, 1908, 23
3302, 743, 21
2857, 1442, 18
2873, 1210, 23
3578, 2138, 25
2975, 2101, 26
2955, 2536, 21
3461, 2589, 12
4651, 2243, 11
3782, 1631, 9
3453, 1913, 13
2812, 1727, 21
3554, 1703, 24
3090, 3194, 25
3528, 3276, 24
3244, 3550, 25
3426, 3850, 20
2869, 2945, 21
3243, 4085, 26
2938, 4485, 24
3151, 4371, 22
3162, 4218, 22
2651, 3601, 26
2681, 4021, 26
2354, 4199, 25
1587, 3307, 26
1055, 3696, 26
1106, 3878, 23
1879, 2965, 18
2008, 2609, 25
1074, 2975, 24
2376, 3108, 21
1266, 2852, 12
1502, 3058, 15
1515, 2552, 24
1889, 1666, 25
2302, 1650, 21
2648, 2358, 24
1769, 1577, 19
2489, 2017, 26
1940, 1745, 16
2662, 2537, 12
2132, 2038, 8
2026, 2118, 5
2774, 1770, 5
2018, 1707, 5
2076, 2656, 6
3445, 1664, 10
3091, 1900, 13
1995, 2116, 21
958, 1755, 24
1178, 1880, 17
1552, 1730, 15
1383, 2203, 17
1657, 2308, 15
845, 2501, 16
2374, 1763, 24
2666, 1098, 24
2353, 981, 23
1336, 814, 24
1043, 608, 24
1794, 592, 18
1609, 982, 15
2730, 1537, 12
2587, 1417, 10
1232, 853, 10
1029, 460, 8
2017, 563, 5
1650, 1107, 7
1747, 1035, 8
929, 1433, 10
2539, 1184, 17
1615, 1220, 19
1466, 503, 26
1194, 3913, 16
1256, 4142, 16
2187, 3882, 12
825, 3388, 10
367, 3663, 7
323, 3753, 25
3121, 3628, 17
3574, 3583, 16
3785, 3192, 12
3160, 2805, 10
2852, 3217, 10
2692, 3099, 10
2635, 3547, 10
3339, 4035, 13
5300, 3924, 14
5097, 4194, 15
5331, 3303, 16
5028, 3495, 14
4300, 2929, 16
4299, 3761, 9
4839, 3594, 7
4786, 3159, 5
4153, 3103, 6
3993, 3865, 6
4383, 1559, 11
4500, 1352, 7
4164, 980, 5
4645, 631, 7
3314, 699, 10
4320, 527, 15
4644, 523, 15
3536, 388, 13
3618, 610, 12
3815, 295, 12
3122, 355, 11
3042, 993, 11
5296, 1230, 11
5226, 2296, 12
5039, 2436, 15
4684, 1851, 13
1092, 2639, 5
1509, 2360, 10
682, 2228, 9
1214, 1704, 7
3231, 1678, 15
3425, 1444, 13
2845, 1312, 14
2284, 1008, 12
4136, 2016, 7
651, 356, 6
370, 266, 13
586, 1401, 20
1177, 297, 15
1859, 3559, 16
1578, 3834, 4
3620, 1665, 14
3588, 2048, 7
4938, 185, 8
4351, 3595, 17
4585, 3916, 20
1758, 4150, 20
786, 1221, 12
48, 3880, 7
66, 3401, 9

3.4 True Positives

TruePositives
5193, 3731, 4
3962, 3348, 4

4 RF

set.seed(317)
rfdat <- data.table(gaba = as.factor(cl$gaba), sfmax)
rf1 <- randomForest(gaba ~ ., data = rfdat)

#set.seed(317)
set.seed(2^13)
train <- sample(nrow(rfdat), 100)
test <- setdiff(1:nrow(rfdat), train)
table(rfdat[test,]$gaba)

## 
##   0   1 
## 123  13

rf2 <- randomForest(gaba ~ ., data = rfdat[train,], importance = TRUE)
print(rf2)

## 
## Call:
##  randomForest(formula = gaba ~ ., data = rfdat[train, ], importance = TRUE) 
##                Type of random forest: classification
##                      Number of trees: 500
## No. of variables tried at each split: 3
## 
##         OOB estimate of  error rate: 10%
## Confusion matrix:
##    0 1 class.error
## 0 90 1  0.01098901
## 1  9 0  1.00000000

rf2.pred <- predict(rf2, newdata = rfdat[test,-c('gaba')])

table(rf2.pred, rfdat[test,]$gaba)

##         
## rf2.pred   0   1
##        0 123  10
##        1   0   3

varImpPlot(rf2)